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biopet.biopet
Commits
6090fa33
Commit
6090fa33
authored
Jun 26, 2014
by
Peter van 't Hof
Browse files
fixed call to sub pipeline
parent
bbc21279
Changes
2
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
6090fa33
...
...
@@ -231,7 +231,7 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
if
(
filename
.
endsWith
(
".gzip"
))
filename
=
filename
.
substring
(
0
,
filename
.
size
-
5
)
if
(
filename
.
endsWith
(
".fastq"
))
filename
=
filename
.
substring
(
0
,
filename
.
size
-
6
)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand
.
output
=
outDir
+
"/"
+
filename
+
"_fastqc.ouput"
fastqcCommand
.
output
=
outDir
+
"/"
+
filename
+
"_fastqc.ou
t
put"
fastqcCommand
.
afterGraph
add
(
fastqcCommand
)
return
fastqcCommand
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
6090fa33
...
...
@@ -109,7 +109,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
flexiprep
.
script
flexiprep
.
init
flexiprep
.
biopetScript
addAll
(
flexiprep
.
functions
)
// Add function of flexiprep to curent function pool
fastq_R1
=
flexiprep
.
outputFiles
(
"output_R1"
)
if
(
paired
)
fastq_R2
=
flexiprep
.
outputFiles
(
"output_R2"
)
...
...
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